8K9O

Crystal structure of Cyanobacteriochrome RcaE GAF domain in Pg state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Green/red light-sensing mechanism in the chromatic acclimation photosensor.

Nagae, T.Fujita, Y.Tsuchida, T.Kamo, T.Seto, R.Hamada, M.Aoyama, H.Sato-Tomita, A.Fujisawa, T.Eki, T.Miyanoiri, Y.Ito, Y.Soeta, T.Ukaji, Y.Unno, M.Mishima, M.Hirose, Y.

(2024) Sci Adv 10: eadn8386-eadn8386

  • DOI: https://doi.org/10.1126/sciadv.adn8386
  • Primary Citation of Related Structures:  
    8K9O

  • PubMed Abstract: 

    Certain cyanobacteria alter their photosynthetic light absorption between green and red, a phenomenon called complementary chromatic acclimation. The acclimation is regulated by a cyanobacteriochrome-class photosensor that reversibly photoconverts between green-absorbing (Pg) and red-absorbing (Pr) states. Here, we elucidated the structural basis of the green/red photocycle. In the Pg state, the bilin chromophore adopted the extended C15- Z , anti structure within a hydrophobic pocket. Upon photoconversion to the Pr state, the bilin is isomerized to the cyclic C15- E , syn structure, forming a water channel in the pocket. The solvation/desolvation of the bilin causes changes in the protonation state and the stability of π-conjugation at the B ring, leading to a large absorption shift. These results advance our understanding of the enormous spectral diversity of the phytochrome superfamily.


  • Organizational Affiliation

    Department of Molecular Biophysics, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
histidine kinase194Microchaete diplosiphonMutation(s): 0 
Gene Names: rcaE
EC: 2.7.13.3
UniProt
Find proteins for Q47897 (Microchaete diplosiphon)
Explore Q47897 
Go to UniProtKB:  Q47897
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47897
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CYC (Subject of Investigation/LOI)
Query on CYC

Download Ideal Coordinates CCD File 
B [auth A]PHYCOCYANOBILIN
C33 H40 N4 O6
VXTXPYZGDQPMHK-GMXXPEQVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.188 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.273α = 90
b = 64.273β = 90
c = 84.116γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan22H02562
Japan Society for the Promotion of Science (JSPS)Japan19K06707
Other privateJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-06-26
    Changes: Database references